For the purposes of testing this specific problem, I edited the apg_feats file and duplicated the "Dastardly Finish" feat several times, renaming each as "DF1, DF2, DF3", and changing the SneakAttack die count required to 1, 2, 3, respectively. This is to show how and when each level is set per class level in rogue.
I then generate a new rogue character of any race. Upon applying the first level, I go to the Feats tab and see DF1 is available as it should be per the requirements (DF2+ are not as should be). Then, I give the character a 2nd level in rogue. I go and look at the feats tab again, and DF1 and still available, DF2+ not available. So far all is correct.
Then, I give a 3rd level in rogue. Going to the feats tab, DF1 is now not available (sneak attack 1 prereq failing), as well as DF2+.
So, I remove one rogue level, taking him back down to 2nd. DF1 is still not available. The only way to fix this is to start a new character or remove all class levels and then re-add the first level. Every time the class level for rogue gets to 3, the Sneak Attack prereq no longer fulfills. It doesn't matter how many levels are added after this.
Windows XP, JRE 1.6
Loading only CRB and APG (with slight modifications, see text for details)